A question about RMSD calculation

From: Chen Yongzhi (yongzhichen_at_hotmail.com)
Date: Thu Mar 04 2004 - 22:54:08 CST

Dear All,

I got a result about RMSD which I could not understand.

First I calculated the RMSD of the first two residue in a protein
seperately. Then I calculated the RMSD of them together. According to my
understanding of RMSD definition, the value of latter should be between
the first two values since it was the some kind of avarage of them. However
the
result is that the value of latter is bigger than both of them. Is this
result possible?

To calculate RMSD, I use tcl script to filter the data from *.dcd file.

Thanks a lot for the help.

Best wishes,
Yongzhi Chen

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